A new sensitive, fast, and robust method using ion chromatography tandem mass spectrometry (IC-MS/MS) for the determination of fosetyl and phosphonic acid in plant-derived matrices was developed. For compensation of matrix effects and differences in recovery rates the isotopically labeled internal standard (ILIS) O-labeled phosphonic acid was added to the samples prior to the extraction of the target compounds. The validation of the method for the matrices tomato, apple, lemon, sultana, avocado, and wheat was performed according to the actual EU guidance document SANTE/11945/2015. The precision and accuracy were determined in five replicates at spiking levels of 0.010 and 0.100 mg/kg with recovery rates between 76 and 105% and RSDs between 1.2 and 17.8%. In this paper, it was achieved for the first time to detect both fosetyl and phosphonic acid at the reporting level of 0.010 mg/kg most relevant for organic plant food commodities.